Tissue-Specific Expression of DNA Methyltransferases Involved in Early-Life Nutritional Stress of Chicken, Gallus gallus

Association between Temperament and Stress-related Gene Expression in Day-old Chickens

Stress in day-old chickens from commercial hatcheries is associated with problematic behavior in adult animals. Recently, we developed a new behavioral handling test for day-old chickens and demonstrated that it assessed temperament differences between seven breeds of native Japanese and Western chickens. In this study, we used 2-day-old male chicks from five of the above breeds to investigate the relationship between temperament and mRNA levels of three stress-related genes (nuclear receptor subfamily 3 group C member 1 (NR3C1), cytochrome P450 family 11 subfamily A member 1, and hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1) involved in the hypothalamic-pituitary-adrenal axis. Principal component analysis of 10 behavioral traits for the handling test revealed that the Fayoumi breed and Hiroshima line of the Chabo breed, both of which exhibited boisterous temperament, clustered separately from the other breeds. Only NR3C1 expression showed a significant positive correlation with two behavioral traits (general vocalization and approaching the wall), and a negative correlation with movement. These results suggest that the complex temperament of day-old chickens is regulated, in part, by stress-related genes along the hypothalamic-pituitary-adrenal axis.

MTK, Orlowski SK. Effects of Environmental Enrichments on Welfare and Hepatic Metabolic Regulation of Broiler Chickens

The aims of this study were to find suitable environmental enrichment (EE) and evaluate the combined effect of two EEs, variable light intensity (VL) lighting program and EH, on mental health and hepatic metabolic regulation in commercial broilers. To find the advantageous EEs for broilers, three different EEs (board, hut, and ramp) were tested in trial 1. EEs were placed and the engagement of birds to EEs, dustbathing behavior, and daily physical activity were observed. Birds treated with huts showed higher engagement than the board- or ramp-treated birds (p < 0.05). The results of dustbathing behavior and daily physical activity indicated that the environmental hut (EH) is the most favorable enrichment for broilers. In the second trial, to test the effect of EHs on mental health and hepatic metabolic conditions, the brain and liver were sampled from the four treatment birds (20 lx_Con, 20 lx_Hut, VL_Con and VL_Hut) on day 42. The lower expression of TPH2 (tryptophan hydroxylase 2) of VL_Hut birds than those of VL_Con and 20 lx_Hut treated birds suggests the combining effect of EHs with the VL lighting program on the central serotonergic homeostasis of broilers. Reduced expressions of TH (tyrosine hydroxylase), GR (glucocorticoid receptor), BDNF (brain-derived neurotrophic factor) of VL_Hut treated birds compared to those of VL_Con and 20 lx_Hut birds suggest lower stress, stress susceptibility, and chronic social stress in VL_Hut treated birds. The expression of CPT1A (carnitine palmitoyl transferase 1) increased over three-fold in the liver of VL_Con birds compared to 20 lx_Con birds (p < 0.05). EHs treatment in VL birds (VL_Hut) significantly decreased CPT1A but not in 20 lx birds (20 lx_Hut). The expression of ACCα (acetyl-CoA carboxylase alpha) was significantly decreased in VL_Con birds compared to 20 lx_Con birds. There was no significant difference in the hepatic FBPase (fructose-1,6-bisphosphatase), GR, and 11β-HSD1 (11 β-hydroxysteroid dehydrogenease-1) expression between 20 lx_Con and VL_Con birds, but EHs significantly stimulated GR in 20 lx_Hut birds, and stimulated FBPase and 11β-HSD1 expression in the VL_Hut birds compared to 20 lx_Con birds, suggesting that the VL lighting program reduced fatty acid synthesis and increased fatty acid β-oxidation in the broilers' liver and VL_Hut improved the hepatic de novo glucose production. Taken together, the results suggest that the stimulated voluntary activity by EHs in the light-enriched broiler house improved mental health and hepatic metabolic function of broilers and may indicate that the improved hepatic metabolic function contributes to efficient nutritional support for broilers.

Biological methylation: redefining the link between genotype and phenotype

The central dogma of molecular biology is responsible for the crucial flow of genetic information from DNA to protein through the transcription and translation process. Although the sequence of DNA is constant in all organs, the difference in protein and variation in the phenotype is mainly due to the quality and quantity of tissue-specific gene expression and methylation pattern. The term methylation has been defined and redefined by various scientists in the last fifty years. There is always huge excitement around this field because the inheritance of something is beyond its DNA sequence. Advanced gene methylation studies have redefined molecular genetics and these tools are considered de novo in alleviating challenges of animal disease and production. Recent emerging evidence has shown that the impact of DNA, RNA, and protein methylation is crucial for embryonic development, cell proliferation, cell differentiation, and phenotype production. Currently, many researchers are focusing their work on methylation to understand its significant role in expression, disease-resistant traits, productivity, and longevity. The main aim of the present review is to provide an overview of DNA, RNA, and protein methylation, current research output from different sources, methodologies, factors responsible for methylation of genes, and future prospects in animal genetics.

Developmental Programming, Evolution, and Animal Welfare: A Case for Evolutionary Veterinary Science

The conditions animals experience during the early developmental stages of their lives can have critical ongoing effects on their future health, welfare, and proper development. In this paper we draw on evolutionary theory to improve our understanding of the processes of developmental programming, particularly Predictive Adaptive Responses (PAR) that serve to match offspring phenotype with predicted future environmental conditions. When these predictions fail, a mismatch occurs between offspring phenotype and the environment, which can have long-lasting health and welfare effects. Examples include metabolic diseases resulting from maternal nutrition and behavioral changes from maternal stress. An understanding of these processes and their evolutionary origins will help in identifying and providing appropriate developmental conditions to optimize offspring welfare. This serves as an example of the benefits of using evolutionary thinking within veterinary science and we suggest that in the same way that evolutionary medicine has helped our understanding of human health, the implementation of evolutionary veterinary science (EvoVetSci) could be a useful way forward for research in animal health and welfare.

Hepatic heat shock proteins, antioxidant-related genes, and immunocompetence of heat-stressed broilers in response to short periods of incubation during egg storage and thermal conditioning

Short Periods of Incubation During Egg Storage (SPIDES) approach improves chick quality and hatching rates. Also, embryonic thermal conditioning (TC) is a strategy for enhancing thermotolerance in avian species. Until now, evaluating the effect of either SPIDES or embryonic TC effects has only been separately conducted, so we hypothesized that combining TC and SPIDES may enhance the response of broilers to thermal stress. Eight hundred Ross broiler eggs were divided into two groups; the first one was kept under appropriate storage room conditions, S0 (control) The 2nd was subjected to SPIDES for 5 h at 37.8 ○C ± 0.1 three times at days 5, 10, and 15 (S1) after egg collection respectively. On the 14th day of incubation (DOI) each of the two main groups was randomly divided into two equal subgroups; the control one was left under the appropriate incubation settings (TC0) whereas the other received prenatal heat conditioning (TC1) at 39.5 ○C ± 0.1 for 6 h/d from the 14th to the 18th embryonic day (E), resulting finally in four experimental subgroups (S0TC0, S1TC0, S0TC1 & S1TC1). RESULTS: showed that SPIDES treatment improved the hatchability of the stored eggs by almost 20% compared to untreated eggs. A combination of SPIDES and TC (S1TC1) increased significantly the levels of Immunoglobulin (IgG and IgM) production at hatch and heat-stressed birds. Our findings revealed that the hepatic heat shock proteins (hsp70, 90 A,90 B, 60 and hspA9), antioxidants-related genes (CAT, and SOD2), and NADPH4 were significantly downregulated in the thermally conditioned group that challenged with thermal stress conditions. As opposed to that, the SPIDES group showed a significant increase in hepatic heat shock proteins, antioxidants-related genes, and NADPH4 when subjected to thermal-stress conditions. In conclusion, the combination of SPIDES and TC has a positive effect on some pre and post-hatch traits of broiler chicks. Under heat stress challenge, thermal conditioning can modify the expression of antioxidant-related genes and Hsps, leading to the enhanced acquisition of thermotolerance as evidenced by lower expression of Hsps and NADPH4. While SPIDES does not have a significant role in thermotolerance acquisition.

Effects of a variable light intensity lighting program on the welfare and performance of commercial broiler chickens

Our previous variable-light intensity lighting program studies indicate the light intensity preference behavior of broilers for their daily activity including eating and resting. To evaluate the effects of variable-light intensity lighting program on performance and welfare of broilers, four commercial trials were conducted for looking at behaviors, mortality, leg-health, performance, and brain welfare indicator genes including tryptophan hydroxylase 2 and tyrosine hydroxylase (TH), glucocorticoid receptor (GR), brain-derived neurotropic factor (BDNF), and melanopsin (Opn4) gene expression. One-day-old broilers were housed in four commercial broiler houses. Each quadrant (section) of the house was placed with 4,800 chicks. A total of four lighting programs began on day 7 with 5 lux (lx), 20 lx, natural light (NL, 480 lx), and variable light (2-5/40 lx) using LED lights on a 16L:8D photoperiod. In the variable-light house, the number of dustbathing holes was significantly higher than that in natural-light houses and 5-lx and 20-lx houses. Daily physical activities, footpad condition, fear response to novel objects, body weight, feed conversion ratio, and the number of leg-problem induced culled birds were affected by the variable-light intensity lighting program. Expression of tryptophan hydroxylase 2 in the DRN and VTA of variable-light treated birds was lower than that of 5-lx- and 20-lx-treated birds on day 42 (p < 0.05). Higher expression of VTA-TH in 5-lx-treated birds than that in 20-lx-, NL-, and variable-light-treated birds suggests the high stress-susceptibility of 5-lx treated birds. Lower VTA-GR expression in 20-lx- and variable-light-treated birds indicates lower stress than that in NL- and 5-lx-treated birds (p < 0.05). The VTA-BDNF expression of NL-treated birds was 2.5 fold higher than that of 5-lx-, 20-lx-, and variable-light-treated birds (p < 0.05), and variable-light-treated birds showed the lowest level of BDNF expression (p < 0.05), suggesting the chronic social defeat stress in NL-treated birds. The result of VTA-Opn4 expression on day 42 suggests the possible role of VTA-Opn4 in broiler welfare through central light perception. Taken together, the variable-light intensity lighting program increased volunteer natural behaviors and physical activity, which may improve footpad condition and leg health of birds, consequently. Performance data including the increased daily weight gain and the lowered feed conversion ratio and results of brain welfare indicator gene expression showed the beneficial effect of the variable-light intensity lighting program on the performance and welfare of commercial broilers.

Growth performance and hepatic antioxidants responses to early thermal conditioning in broiler chickens

There are little data about antioxidants' status responses to early thermal conditioning (TC) on broiler chickens. Therefore, the present study was conducted to investigate the different time ages of thermal conditioning on antioxidants responses and the growth rate of broiler chicks. A total of two hundred forty-one-day-old male broiler chicks (Cobb 500) weighed on average 51.5 ± 0.5g were randomly distributed into four equal groups (60 chicks each), and chicks of each group were ranked in five replicates. The first group reared under the ambient temperature, while the second, third and fourth groups (TC3, TC5 and TC7) were subjected to early-age thermal conditioning at 39°C for 6 h on the third, fifth and seventh day of age respectively. Broilers were fed ad-libitum, and drinking water was a free choice during the experimental period. At the end of the experimental period that lasted 5 weeks, all experimental groups were exposed to heat challenge at 36°C for 6 h. Early-age thermal conditioning did not affect growth performance. Plasma corticosterone elevation in TC5 (as a post-challenge response) was the lowest among the experimental groups. Hepatic malondialdehyde significantly increased in TC5 and TC7 groups both at the post-conditioning stage and at the end of the experimental period. Hepatic glutathione, glutathione S-transferases, catalase and superoxide dismutase significantly decreased by early-age thermal conditioning compared with non-conditioned broilers. Microscopic examination of the liver sections from broilers chickens in TC5 and TC7 groups showed all the basic features of normal liver tissue, while the control and TC3 groups showed few necrotic areas. It could be concluded that early-age thermal conditioning at 39°C for 6 h on the fifth day of age could improve the antioxidant defence system of broilers without any adverse effects on growth performance.

Effects of a variable light intensity lighting program on the welfare and performance of commercial broiler chickens

Our previous variable-light intensity lighting program studies indicate the light intensity preference behavior of broilers for their daily activity including eating and resting. To evaluate the effects of variable-light intensity lighting program on performance and welfare of broilers, four commercial trials were conducted for looking at behaviors, mortality, leg-health, performance, and brain welfare indicator genes including tryptophan hydroxylase 2 and tyrosine hydroxylase (TH), glucocorticoid receptor (GR), brain-derived neurotropic factor (BDNF), and melanopsin (Opn4) gene expression. One-day-old broilers were housed in four commercial broiler houses. Each quadrant (section) of the house was placed with 4,800 chicks. A total of four lighting programs began on day 7 with 5 lux (lx), 20 lx, natural light (NL, 480 lx), and variable light (2-5/40 lx) using LED lights on a 16L:8D photoperiod. In the variable-light house, the number of dustbathing holes was significantly higher than that in natural-light houses and 5-lx and 20-lx houses. Daily physical activities, footpad condition, fear response to novel objects, body weight, feed conversion ratio, and the number of leg-problem induced culled birds were affected by the variable-light intensity lighting program. Expression of tryptophan hydroxylase 2 in the DRN and VTA of variable-light treated birds was lower than that of 5-lx- and 20-lx-treated birds on day 42 (p < 0.05). Higher expression of VTA-TH in 5-lx-treated birds than that in 20-lx-, NL-, and variable-light-treated birds suggests the high stress-susceptibility of 5-lx treated birds. Lower VTA-GR expression in 20-lx- and variable-light-treated birds indicates lower stress than that in NL- and 5-lx-treated birds (p < 0.05). The VTA-BDNF expression of NL-treated birds was 2.5 fold higher than that of 5-lx-, 20-lx-, and variable-light-treated birds (p < 0.05), and variable-light-treated birds showed the lowest level of BDNF expression (p < 0.05), suggesting the chronic social defeat stress in NL-treated birds. The result of VTA-Opn4 expression on day 42 suggests the possible role of VTA-Opn4 in broiler welfare through central light perception. Taken together, the variable-light intensity lighting program increased volunteer natural behaviors and physical activity, which may improve footpad condition and leg health of birds, consequently. Performance data including the increased daily weight gain and the lowered feed conversion ratio and results of brain welfare indicator gene expression showed the beneficial effect of the variable-light intensity lighting program on the performance and welfare of commercial broilers.

Nutrigenomics in livestock sector and its human-animal interface-a review

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Nutrigenomics unfolds the link between nutrition and gene expression for productivity.expression profile of intramuscular.

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Nutrigenomics helps scientists discover genes and DNA in each animal's cell or tissue by assisting them in selecting nutrients.

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It brings out the importance of micronutrition for increasing animal production.

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Nutrigenomics integrates nutrition, molecular biology, genomics, bioinformatics, molecular medicine, and epidemiology.

Noncommunicable diseases such as cardiovascular disease, obesity, diabetes, and cancer now outnumber all other health ailments in humans globally due to abrupt changes in lifestyle following the industrial revolution. The industrial revolution has also intensified livestock farming, resulting in an increased demand for productivity and stressed animals. The livestock industry faces significant challenges from a projected sharp increase in global food and high animal protein demand. Nutrition genomics holds great promise for the future as its advances have opened up a whole new world of disease understanding and prevention. Nutrigenomics is the study of the interactions between genes and diet. It investigates molecular relationships between nutrients and genes to identify how even minor modifications could potentially alter animal and human health/performance by using techniques like proteomics, transcriptomics, metabolomics, and lipidomics. Dietary modifications mostly studied in livestock focus mainly on health and production traits through protein, fat, mineral, and vitamin supplementation changes. Nutrigenomics meticulously selects nutrients for fine-tuning the expression of genes that match animal/human genotypes for better health, productivity, and the environment. As a step forward, nutrigenomics integrates nutrition, molecular biology, genomics, bioinformatics, molecular medicine, and epidemiology to better understand the role of food as an epigenetic factor in the occurrence of these diseases. This review aims to provide a comprehensive overview of the fundamental concepts, latest advances, and studies in the field of nutrigenomics, emphasizing the interaction of diet with gene expression, and how it relates to human and animal health along with its human-animal interphase.

Dietary L-citrulline modulates the growth performance, amino acid profile, and the growth hormone/insulin-like growth factor axis in broilers exposed to high temperature

Heat stress adversely affects the growth performance, muscle development, and protein metabolism in poultry. l-Citrulline (L-Cit), is a non-essential amino acid that is known to stimulate muscle protein synthesis under stress conditions. This study investigated whether L-Cit could influence the growth performance, amino acid profile, and protein metabolism in broilers exposed to high ambient temperature. In a 2 × 2 factorial arrangement, Arbor acre broilers (288 chickens) were fed with basal diet (CON) or 1% L-Cit supplemented diet and later subjected to either thermoneutral (TNZ: 24°C, 24 h/d) or heat stress (HS: 35°C for 8 h/d) environment for 21 days. The results showed that L-Cit diet promoted the body weight and body weight gain of broilers higher than the CON diet, and it further alleviated HS suppression of body weight and feed intake at certain periods (p &lt; 0.05). Plasma urea, uric acid, glucose, and total cholesterol were elevated during HS, whereas, the triglyceride content was decreased (p &lt; 0.05). Serum amino acids including citrulline, alanine, aspartate, and taurine were decreased by HS. L-Cit supplementation restored the citrulline level and alleviated HS induction of 3-methylhistidine (p &lt; 0.05). L-Cit supplementation increased the plasma growth hormone (GH) and insulin-like growth factor-1 (IGF-1) concentration, as well as the GH concentration in the breast muscle (p &lt; 0.05). The mRNA expression showed that HS elicited tissue-specific responses by upregulating some growth factors in the breast muscle, but downregulated the GH receptor, GH binding protein, and IGF-1 expression in the hypothalamus. L-Cit supplementation upregulated the GHRH and IGFBP2 expression in the hypothalamus. L-Cit also upregulated the expression of IGF-1R and IGFBP2 in the breast muscle of HS broilers. The total mTOR protein level in the breast muscle of HS broilers was also increased by L-Cit diet (p &lt; 0.05). Therefore, this study demonstrated that HS negatively affected the growth performance of broilers and dysregulated the expression of growth factors related to protein metabolism. Contrarily, L-Cit promoted the growth responses of broilers via its stimulation of circulating GH/IGF-1 concentration. To certain extents, L-Cit supplementation elicited protective effects on the growth performance of HS broilers by diminishing protein catabolism.

Synergy Between Dietary Quercetin and Vitamin E Supplementation in Aged Hen’s Diet Improves Hatching Traits, Embryo Quality, and Antioxidant Capacity of Chicks Hatched From Eggs Subjected to Prolonged Storage

The current study aims to investigate the effects of the synergy between quercetin and vitamin E in aged hen’s diet on hatchability and antioxidant levels of the embryo and newly hatched chicks from prolonged storage eggs. A total of 400 breeder laying hens of 65 weeks of age were selected and randomly divided into 4 groups. Birds were fed a basal diet alone (Control), and basal diets supplemented with quercetin (Q) (0.4 g/kg) and vitamin E (VE) (0.2 g/kg) alone and their combination (0.4 g/kg Q + 0.2 g/kg VE) for 14 weeks, respectively, to determine their effects on yolk antioxidant status, fertility, embryonic mortality, hatchability, antioxidant status of embryonic tissues, as well as the antioxidant status of the newly hatched chicks. The results showed that the hen’s dietary Q + VE increased the yolk weight, as well as increased the antioxidant status of the egg yolk (p < 0.05). Compared with the control group, the supplementation of Q + VE significantly increased the hatchability of set-fertile eggs and decreased early embryonic mortality in eggs stored for 7 and 14 days, respectively (p < 0.05), and also improved the antioxidant capacity of the embryos obtained from eggs stored for 14 days (before incubation) (p < 0.05). Moreover, Q + VE increased the levels of SOD, GSH-Px, T-AOC, T-SOD, and CAT in the liver, heart, and pectoral muscle of the embryo, 1-day-old and 14-day-old chicks (p < 0.05), as well as upregulated the antioxidant related genes (GPx-1, GPx-2, GPx-4, DIO-1, and SOD-1) in the liver of the embryo, 1-day-old and 14-day-old chicks hatched from 14-days storage eggs (p < 0.05). Meanwhile, the MDA levels were decreased by the Q + VE in the embryo and post-hatched chicks (p < 0.05). In conclusion, these findings suggested that maternal dietary Q + VE exerts beneficial synergistic effects on the antioxidant capacity of the egg yolk, embryo, and chicks during prolong egg storage, therefore, Q + VE could be used as a dietary measure to enhance hatchability and chick quality in poultry production.

DNA Methylation and Detoxification in the Earthworm Lumbricus terrestris Exposed to Cadmium and the DNA Demethylation Agent 5-aza-2'-deoxycytidine

Earthworms are well-established model organisms for testing the effects of heavy metal pollution. How DNA methylation affects cadmium (Cd) detoxification processes such as the expression of metallothionein 2 (MT2), however, is largely unknown. We therefore exposed Lumbricus terrestris to 200 mg concentrations of Cd and 5-aza-2'-deoxycytidine (Aza), a demethylating agent, and sampled tissue and coelomocytes, cells of the innate immune system, for 48 h. MT2 transcription significantly increased in the Cd- and Cd-Aza-treated groups. In tissue samples, a significant decrease in MT2 in the Aza-treated group was detected, showing that Aza treatment inhibits basal MT2 gene activity but has no effect on Cd-induced MT2 levels. Although Cd repressed the gene expression of DNA-(cytosine-5)-methyltransferase-1 (DNMT1), which is responsible for maintaining DNA methylation, DNMT activity was unchanged, meaning that methylation maintenance was not affected in coelomocytes. The treatment did not influence DNMT3, which mediates de novo methylation, TET gene expression, which orchestrates demethylation, and global levels of hydroxymethylcytosine (5hmC), a product of the demethylation process. Taken together, this study indicates that Aza inhibits basal gene activity, in contrast to Cd-induced MT2 gene expression, but does not affect global DNA methylation. We therefore conclude that Cd detoxification based on the induction of MT2 does not relate to DNA methylation changes.

Exogenous Linoleic Acid Intervention Alters Hepatic Glucose Metabolism in an Avian Embryo Model

In the present study, developmental changes of gluconeogenesis and glycolysis in an avian model were measured, and then the intervention effects of in ovo feeding (IOF) linoleic acid (LA) on hepatic glucose metabolism were evaluated. In Experiment 1, thirty fertilized eggs were sampled on embryonic days (E) of 16, 19, 22, 25, 28, 31, and thirty newly-hatched ducklings at hatch (E34 and E35). In Experiment 2, a total of 120 fertilized eggs (60 eggs for each group) were injected into the yolk sac with PBS as the control group and LA as the IOF LA group on E25. Twelve eggs were selected for sample collection on E28 and E31. Serum contents of glucose, pyruvate, and lactate increased ( p < 0.05) linearly or quadratically from E16 to hatch, as well as hepatic glycogen and pyruvate contents. Hepatic mRNA expression related to energy homeostasis, gluconeogenesis, and glycolysis increased ( p < 0.05) in embryogenesis, and the plateau period was presented on E25–E31. IOF LA decreased ( p < 0.05) serum contents of glucose, triacylglycerol, cholesterol, and hepatic oleic acid, unsaturated fatty acids on E28, as well as the gene expression relative to gluconeogenesis. IOF LA increased ( p < 0.05) pyruvate content in serum and liver, and hepatic gene expression relative to glycolysis on E31. In summary, hepatic gluconeogenesis and glycolysis were enhanced to meet the increasing energy demands of embryonic development during E25 – hatch. Exogenous LA intervention on E25 could inhibit hepatic gluconeogenesis and enhance glycolysis during the later developmental period, disrupting glucose embryonic homeostasis and energy status.

Analysis of Genomic Alternative Splicing Patterns in Rat under Heat Stress Based on RNA-Seq Data

Heat stress is one of the most severe challenges faced in livestock production in summer. Alternative splicing as an important post-transcriptional regulation is rarely studied in heat-stressed animals. Here, we performed and analyzed RNA-sequencing assays on the liver of Sprague-Dawley rats in control (22 °C, n = 5) and heat stress (4 °C for 120 min, H120; n = 5) groups, resulting in the identification of 636 differentially expressed genes. Identification analysis of the alternative splicing events revealed that heat stress-induced alternative splicing events increased by 20.18%. Compared with other types of alternative splicing events, the alternative start increased the most (43.40%) after heat stress. Twenty-eight genes were differentially alternatively spliced (DAS) between the control and H120 groups, among which Acly, Hnrnpd and mir3064 were also differentially expressed. For DAS genes, Srebf1, Shc1, Srsf5 and Ensa were associated with insulin, while Cast, Srebf1, Tmem33, Tor1aip2, Slc39a7 and Sqstm1 were enriched in the composition of the endoplasmic reticulum. In summary, our study conducts a comprehensive profile of alternative splicing in heat-stressed rats, indicating that alternative splicing is one of the molecular mechanisms of heat stress response in mammals and providing reference data for research on heat tolerance in mammalian livestock.

Mitigating the detrimental effects of heat stress in poultry through thermal conditioning and nutritional manipulation

The poultry industry faces several obstacles and challenges, including the changes in global temperature, increase in the per capita demand for meat and eggs, and the emergence and spread of various diseases. Among these, environmental challenges are one of the most severe hurdles impacting the growth and productivity of poultry. In particular, the increasing frequency and severity of heat waves over the past few years represent a major challenge, and this is expected to worsen in the coming decades. Chickens are highly susceptible to high ambient temperatures (thermal stress), which negatively affect their growth and productivity, leading to enormous economic losses. In the light of global warming, these losses are expected to increase in the near future. Specifically, the worsening of climate change and the rise in global temperatures have augmented the adverse effects of heat on poultry production worldwide. At present, the world population is approximately 7.9 billion, and it has been predicted to reach 9.3 billion by 2050 and approximately 11 billion by 2100, implying a great demand for protein supply; therefore, strategies to mitigate future poultry challenges must be urgently devised. To date, several mitigation measures have been adopted to minimize the negative effects of heat stress in poultry. Of these, thermal acclimation at the postnatal stage or throughout the embryonic stages has been explored as a promising approach; however, for large-scale application, this approach warrants further investigation to determine the suitable temperature and poultry age. Moreover, molecular mechanisms governing thermal conditioning are poorly understood. To this end, we sought to expand our knowledge of thermal conditioning in poultry, which may serve as a valuable reference to improve the thermotolerance of chickens via nutritional management and vitagene regulation. Vitagenes regulate the responses of poultry to diverse stresses. In recent years, nutritionists have paid close attention to bioactive compounds such as resveratrol, curcumin, and quercetin administered alone or in combination. These compounds activate vitagenes and other regulators of the antioxidant defense system, such as nuclear factor-erythroid 2-related factor 2. Overall, thermal conditioning may be an effective strategy to mitigate the negative effects of heat stress. In this context, the present review synthesizes information on the adverse impacts of thermal stress, elucidating the molecular mechanisms underlying thermal conditioning and its effects on the acquisition of tolerance to acute heat stress in later life. Finally, the role of some polyphenolic compounds, such as resveratrol, curcumin, and quercetin, in attenuating heat stress through the activation of the antioxidant defense system in poultry are discussed.

mRNA Expressions of Methylation Related Enzymes and Duration of Thermal Conditioning in Chicks

DNA methylation regulates gene expression by modifying the nucleosome structure of DNA, without altering the gene sequence. It has been reported that DNA methylation reactions are catalyzed by several enzymes. In chickens, thermal conditioning treatment affects the central DNA methylation levels. The purpose of this study was to clarify the changes in DNA methylation and demethylation factors during thermal conditioning in the hypothalamus of 3-day-old chicks. Male chicks (3-days old) were exposed to 40±0.5°C as a thermal conditioning treatment for 1, 2, 6, 9, or 12 h. The control chicks were kept in a thermoneutral zone (30±0.2°C). After thermal conditioning, the mRNA levels of DNA methyltransferase (DNMT)-1, -3a, -3b, and ten-eleven translocation (TET)-1, -2, and -3 in the hypothalamus were measured by q-PCR. The mRNA levels of DNMT-3a and TET-1 were increased by thermal conditioning. Moreover, the expression level of TET-1 increased with the loading time of the thermal conditioning. The gene expressions of DNMT-1, DNMT-3b, TET-2, and TET-3 were not affected by thermal conditioning. Since DNMT-3a is a catalyst for de-novo DNA methylation and TET-1 catalyzes the oxidation of methylated cytosine, it is suggested that the thermal conditioning increased the activation of DNA methylation and demethylation factors, which occur in the hypothalamus of neonatal chicks.

Impacts of Embryonic Thermal Programming on the Expression of Genes Involved in Foie gras Production in Mule Ducks

Embryonic thermal programming has been shown to improve foie gras production in overfed mule ducks. However, the mechanisms at the origin of this programming have not yet been characterized. In this study, we investigated the effect of embryonic thermal manipulation (+1°C, 16 h/24 h from embryonic (E) day 13 to E27) on the hepatic expression of genes involved in lipid and carbohydrate metabolisms, stress, cell proliferation and thyroid hormone pathways at the end of thermal manipulation and before and after overfeeding (OF) in mule ducks. Gene expression analyses were performed by classic or high throughput real-time qPCR. First, we confirmed well-known results with strong impact of OF on the expression of genes involved in lipid and carbohydrates metabolisms. Then we observed an impact of OF on the hepatic expression of genes involved in the thyroid pathway, stress and cell proliferation. Only a small number of genes showed modulation of expression related to thermal programming at the time of OF, and only one was also impacted at the end of the thermal manipulation. For the first time, we explored the molecular mechanisms of embryonic thermal programming from the end of heat treatment to the programmed adult phenotype with optimized liver metabolism.

The Full-Length Transcriptome Provides New Insights Into the Transcript Complexity of Abdominal Adipose and Subcutaneous Adipose in Pekin Ducks

Adipose tissues have a central role in organisms, and adipose content is a crucial economic trait of poultry. Pekin duck is an ideal model to study the mechanism of abdominal and subcutaneous adipose deposition for its high ability of adipose synthesis and deposition. Alternative splicing contributes to functional diversity in abdominal and subcutaneous adipose. However, there has been no systematic analysis of the dynamics of differential alternative splicing of abdominal and subcutaneous adipose in Pekin duck. In our study, the Pacific Biosciences (PacBio) Iso-Seq technology was applied to explore the transcriptional complexity of abdominal and subcutaneous adipose in Pekin ducks. In total, 143,931 and 111,337 full-length non-chimeric transcriptome sequences of abdominal and subcutaneous adipocytes were obtained from 41.78 GB raw data, respectively. These data led us to identify 19,212 long non-coding RNAs (lncRNAs) and 74,571 alternative splicing events. In addition, combined with the next-generation sequencing technology, we correlated the structure and function annotation with the differential expression profiles of abdominal and subcutaneous adipose transcripts. This study identified lots of novel alternative splicing events and major transcripts of transcription factors related to adipose synthesis. STAT3 was reported as a vital gene for adipogenesis, and we found that its major transcript is STAT3-1, which may play a considerable role in the process of adipose synthesis in Pekin duck. This study greatly increases our understanding of the gene models, genome annotations, genome structures, and the complexity and diversity of abdominal and subcutaneous adipose in Pekin duck. These data provide insights into the regulation of alternative splicing events, which form an essential part of transcript diversity during adipogenesis in poultry. The results of this study provide an invaluable resource for studying alternative splicing and tissue-specific expression.

Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

Background

DNA methylation is likely a key mechanism regulating changes in gene transcription in traits that show temporal fluctuations in response to environmental conditions. To understand the transcriptional role of DNA methylation we need simultaneous within-individual assessment of methylation changes and gene expression changes over time. Within-individual repeated sampling of tissues, which are essential for trait expression is, however, unfeasible (e.g. specific brain regions, liver and ovary for reproductive timing). Here, we explore to what extend between-individual changes in DNA methylation in a tissue accessible for repeated sampling (red blood cells (RBCs)) reflect such patterns in a tissue unavailable for repeated sampling (liver) and how these DNA methylation patterns are associated with gene expression in such inaccessible tissues (hypothalamus, ovary and liver). For this, 18 great tit (Parus major) females were sacrificed at three time points (n = 6 per time point) throughout the pre-laying and egg-laying period and their blood, hypothalamus, ovary and liver were sampled.

Results

We simultaneously assessed DNA methylation changes (via reduced representation bisulfite sequencing) and changes in gene expression (via RNA-seq and qPCR) over time. In general, we found a positive correlation between changes in CpG site methylation in RBCs and liver across timepoints. For CpG sites in close proximity to the transcription start site, an increase in RBC methylation over time was associated with a decrease in the expression of the associated gene in the ovary. In contrast, no such association with gene expression was found for CpG site methylation within the gene body or the 10 kb up- and downstream regions adjacent to the gene body.

Conclusion

Temporal changes in DNA methylation are largely tissue-general, indicating that changes in RBC methylation can reflect changes in DNA methylation in other, often less accessible, tissues such as the liver in our case. However, associations between temporal changes in DNA methylation with changes in gene expression are mostly tissue- and genomic location-dependent. The observation that temporal changes in DNA methylation within RBCs can relate to changes in gene expression in less accessible tissues is important for a better understanding of how environmental conditions shape traits that temporally change in expression in wild populations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07329-9.

Effects of light intensity and dual light intensity choice on plasma corticosterone, central serotonergic and dopaminergic activities in birds, Gallus gallus

Light intensity plays an important role in the regulation of growth, behavior, reproduction, and welfare of avian species. Light intensity preference behavior has been suggested to be involved in welfare of birds. This study aims to investigate the effects of different light intensity and dual light intensity choice (DLIC) lighting program on plasma corticosterone (CORT), and tryptophan hydroxylase 2 (TPH2, the rate-limiting enzyme of serotonin biosynthesis) and tyrosine hydroxylase (TH, the rate-limiting enzyme of dopamine biosynthesis) gene expression in the brainstem of male chickens. Day old broilers were housed in two commercial houses, and placed in 24 pens. All the treatment groups were provided with 23 h light (L) /1 h dark (D) and 30 lx (lx) light intensity during the first week and then 18L:6D (10 lx) from day 7 to 14. Blood and brain were sampled at 14 days of age (10 lx) before the onset of light treatments. On day 15, four treatments (2, 10, 20, and 100 lx), and DLIC treatment (2/20 lx) were initiated. Samples were collected on days 15, 16, 17, 30 and 41. TPH2 expression in the dorsal raphe nucleus (DRN) and caudal raphe nucleus (CRN) of brainstem, and TPH2 and TH expression in ventral tegmental areas (VTN) of the midbrain were determined by qPCR. Results showed that bright light and DLIC lighting program temporarily attenuated plasma CORT, suggesting the short-term stress attenuating effect of bright light and DLIC lighting program. Differential TPH2 expression in the DRN and CRN observed in the DLIC birds indicate a significant effect of DLIC lighting program on the serotonergic activity in the avian brainstem. At the 41 days of age, the significant downregulation of TPH2 and TH expression occurred in the VTA of DLIC treated birds compared to the other group of birds. Taken together, temporal and spatial regulation of TPH2 and TH expression by DLIC lighting program indicate that compensatory regulation of serotonergic and dopaminergic activities might be involved in the light intensity preference behavior of birds, suggesting a possible beneficial effect of the DLIC lighting program on broiler welfare.

Effect of transportation and shackling on plasma concentrations of corticosterone and heterophil to lymphocyte ratios in market weight male turkeys in a commercial operation

There is limited information on the effects of stress and/or physiological manipulation on either plasma concentrations of corticosterone (CORT) and/or heterophil: lymphocyte (H : L) ratios in turkeys. The present studies examine the effects of catching/transportation/lairage in a holding shed and shackling on plasma concentrations of CORT and H : L ratios in male market weight turkeys. Plasma concentrations of CORT were increased after transportation and lairage but not further elevated by shackling, irrespective of its duration up to 240 s. In one study, there were increased H : L ratios following catching/placing birds into transportation cages/transportation/lairage. In one study, H : L ratios declined following shackling. It is concluded that while moving turkeys from the farm to immediately before the shackling line is stressful, shackling for up to 4 min was not perceived as more stressful in turkeys. There were also differences between farms/houses for both plasma concentrations of CORT and H : L ratios.

Changes in DNA methylation and histone modification gene expression in response to daily food times in zebra finches: epigenetic implications

We hypothesized that daily food availability times served as an ‘epigenetic’ factor and affected the reproductive physiology in continuously reproducing species. This we tested by measurement of mRNA expression of genes coding for the enzymes involved in DNA methylation-demethylation (dnmts, tets) and histone modification (hat1, hdacs) in the hypothalamus, liver and gonads of male and female zebra finches that were paired held for a year under 12L:12D with access to the time-restricted food availability (TrF: 4-h in morning, TrF-M, or evening, TrF-E) with controls on food ad libitum (FAL). The overall hypothalamic and hepatic expression patterns of hat1 and hdac(s) were similar but those of dnmt(s) and tet(s) were different between males and females. Irrespective of TrF timings, both hat1 and hdac(s) mRNA levels were increased in the hypothalamus, but not in liver in which hat1 mRNA levels were increased in the TrF-M group. While hypothalamic tet(s) were higher in TrF-E males, the hepatic tet(s) were higher in TrF-M birds (tet1, only males). Gonadal expressions were further varied and showed sex differences. Histone modifying genes did not show TrF-effects, except the elevated testicular hdac3 levels. Similarly, testicular dnmt3b and tet2 mRNA levels were increased and decreased in TrF-M and TrF-E, respectively, whereas ovarian dnmt1 and tet2 levels were reduced in TrF-M and tet1 in the TrF-E. Present results suggest that an enforced daily feeding schedule in long term could serve as a conditioning environment that shapes at epigenetic levels, the overall hypothalamic regulation, liver and gonadal functions in diurnal vertebrates.

The vasotocinergic system and its role in the regulation of stress in birds

The regulation of stress in birds includes a complex interaction of neural systems affecting the hypothalamic-pituitary-adrenal (HPA) axis. In addition to the hypothalamic paraventricular nucleus, a structure called the nucleus of the hippocampal commissure likewise affects the output of pituitary stress hormones and appears to be unique to avian species. Within the anterior pituitary, the avian V1a and V1b receptors were found in corticotropes. Based on our studies with central administration of hormones in the chicken, corticotropic releasing hormone (CRH) is a more potent ACTH secretagogue than arginine vasotocin (AVT). In contrast, when applied peripherally, AVT is more efficacious. Co-administration of AVT and CRH peripherally, resulted in a synergistic stimulation of corticosterone release. Data suggest receptor oligomerization as one possible mechanism. In birds, vasotocin receptors associated with stress responses include the V1a and V1b receptors. Three-dimensional, homology-based structural models of the avian V1aR were built to test agonists and antagonists for each receptor that were screened by molecular docking to map their binding sites on each receptor. Additionally, binding affinity values for each available peptide antagonist to the V1aR and V1bR were determined. An anterior pituitary primary culture system was developed to determine how effective each antagonist blocked the function of each receptor in culture when stimulated by a combination of AVT/CRH administration. Use of an antagonist in subsequent in vivo studies identified the V1aR in regulating food intake in birds. The V1aR was likewise found in circumventricular organs of the brain, suggesting a possible function in stress.

Epigenetic Mechanisms of the Glucocorticoid Receptor

The glucocorticoid receptor (GR) has been shown to be important for mediating cellular responses to stress and circulating glucocorticoids. Ligand-dependent transcriptional changes induced by GR are observed across numerous tissues. However, the mechanisms by which GR achieves cell and tissue-specific effects are less clear. Epigenetic mechanisms have been proposed to explain some of these differences as well as some of the lasting, even transgenerational, effects of stress and glucocorticoid action. GR functions in tandem with epigenetic cellular machinery to coordinate transcription and shape chromatin structure. Here, we describe GR interactions with these effectors and how GR acts to reshape the epigenetic landscape in response to the environment.

Yolk immunoreactive corticosterone in hierarchical follicles of Japanese quail (Coturnix japonica) exposed to heat challenge

High temperature decreases the egg number, ovarian weight, and hierarchical follicle number. In the present study, we investigated the effect of high temperature on the quality of eggs of adult female quails. Laying quail were raised under a standard thermal condition of 25 °C until exposed to an elevated temperature of 34 °C (experimental) or maintained at 25 °C (control) from 12:00 to 16:00 for 10 consecutive days. Weight and number of eggs were measured; serum and the largest follicles were collected and used for hormone measurement. Ovaries and adrenals were collected for expression analysis of 3β- and 17β-HSD, genes encoding steroidogenic enzymes. Egg weight slightly decreased with an increase in the treatment time in the heat-challenged group; the egg weight significantly decreased in the heat treatment group than in the control group during the last 2 days of experiment (P < 0.05). The laying rate showed no difference during the experimental period but significantly decreased on the last day in the heat treatment group. In the experimental group the ovaries and oviducts were lighter (P < 0.05) and the hierarchical follicle number and ovarian weight decreased (P < 0.05) compared to the control group. Although serum corticosterone level significantly increased after heat challenge (P < 0.05) and immediately recovered to the normal level, yolk immunoreactive corticosterone in the hierarchical follicle (F1, F2, F3) significantly increased (P < 0.05). The expression level of 17β-HSD showed no changes in the ovary but significantly increased in adrenals (P < 0.05). Our findings indicate that the effects of heat challenge on the maternal ovary in the quail are mediated through the adrenal function.

Epigenome-wide methylation differences in a group of lean and obese women - A HUNT Study

Knowledge of epigenetically regulated biomarkers linked to obesity development is still scarce. Improving molecular understanding of the involved factors and pathways would improve obesity phenotype characterization and reveal potentially relevant targets for obesity intervention. The Illumina Infinium HumanMethylation450 BeadChip was used in a leucocyte epigenome-wide association study (EWAS) to quantify differential DNA methylation in 60 lean compared with 60 obese young women. Replication was done in monozygotic twins discordant for obesity. At adolescence and adulthood, the two weight groups differed significantly in obesity-related traits and metabolic risk factors. Differential hypomethylation was overrepresented in obese compared to lean women. In the adjusted model, the EWAS revealed 10 differentially methylated CpG sites linked to 8 gene loci – COX6A1P2/FGD2, SBNO2, TEX41, RPS6KA2, IGHE/IGHG1/IGHD, DMAP1, SOCS3, and SETBP1– and an enhancer locus at chromosome 2 (2p25.1). The sites linked to TEX41, IGHE/IGHG1/IGHD, DMAP1, and SETBP1 were novel findings, while COX6A1P/FGD2, SBNO2, RPS6KA2, and SOCS3 had been identified previously with concordant direction of effects. RPS6KA2, DMAP1, and SETBP1 were replicated in the BMI-discordant monozygotic twin cohort using the FDR of 5%.

A Novel Dnmt3a1 Transcript Inhibits Adipogenesis

DNA (cytosine-5)-methyltransferase 3a (Dnmt3a) is an enzyme that catalyzes the transfer of methyl groups to specific CpG forms in DNA. In mammals, two variant transcripts of Dnmt3a have been successfully identified. To the best of our knowledge, no Dnmt3a transcripts in an avian have been successfully identified. This study was performed to detect different transcripts of Dnmt3a in chickens and to examine whether a novel Dnmt3a transcript named Dnmt3a1 may regulate adipogenesis. In addition to cloning, sequencing, transcript detection, and expression studies, a novel Dnmt3a1 transcript overexpression and knockdown were conducted to explore the potential role of Dnmt3a1 in preadipocyte proliferation and the early stage of adipocyte differentiation. In chicken abdominal fat tissue, we detected a novel Dnmt3a1 transcript that differs from Dnmt3a by lacking 23 amino acids at the exon-1/exon-2 border. Dnmt3a1 mRNA was ubiquitously expressed in a variety of tissues or cells and highly expressed in chicken adipose tissue/cells. The expression of Dnmt3a1 was regulated under different physiological conditions including aging, fasting, and high-fat diet. In addition, overexpression of Dnmt3a1 significantly decreased preadipocyte proliferation and induced cell-cycle arrest while its inhibition increased cell proliferation and S-phase cells. Furthermore, the overexpression of Dnmt3a1 significantly upregulated the mRNA level of cell-cycle-related genes, such as CDKN1A, CDKN1B, CCNB3, CCND2, CCNG2, CDKN2B, and CDK9, or the protein level of CDKN1A, CDKN1B, and CCNG2. Conversely, the knockdown of Dnmt3a1 by siRNA had the opposite effects. Moreover, during early adipocyte differentiation, the overexpression of Dnmt3a1 significantly decreased the mRNA and the protein levels of PPAR-γ, C/EBP-α, ADIPOR1, and STAT3, and the mRNA levels of FAS, LEPR, LPL, PRKAB2, and ATGL. In contrast, their expression was significantly increased after the knockdown of Dnmt3a1. Taken together, we identified a novel transcript of Dnmt3a, and it played a potential role in adipogenesis.

Epigenetic and redox biomarkers: Novel insights from the MARK-AGE study

Ageing is a multifactorial process that affects most, if not all, of the body's tissues and organs and can be defined as the accumulation of physical and psychological changes in a human being over time. The rate of ageing differs between individuals of the same chronological age, meaning that 'biological age' of a person may be different from 'chronological age'. Furthermore, ageing represents a very potent risk factor for diseases and disability in humans. Therefore, establishment of markers of biological ageing is important for preventing age-associated diseases and extending health span. MARK-AGE, a large-scale European study, aimed at identifying a set of biomarkers which, as a combination of parameters with appropriate weighting, would measure biological age better than any marker in isolation. But beyond the identification of useful biomarkers, MARK-AGE provided new insights in age-associated specific cellular processes, such as DNA methylation, oxidative stress and the regulation of zinc homeostasis.

Effect of Morinda citrifolia (Noni)-Enriched Diet on Hepatic Heat Shock Protein and Lipid Metabolism-Related Genes in Heat Stressed Broiler Chickens

Heat stress (HS) has been reported to alter fat deposition in broilers, however the underlying molecular mechanisms are not well-defined. The objectives of the current study were, therefore: (1) to determine the effects of acute (2 h) and chronic (3 weeks) HS on the expression of key molecular signatures involved in hepatic lipogenic and lipolytic programs, and (2) to assess if diet supplementation with dried Noni medicinal plant (0.2% of the diet) modulates these effects. Broilers (480 males, 1 d) were randomly assigned to 12 environmental chambers, subjected to two environmental conditions (heat stress, HS, 35°C vs. thermoneutral condition, TN, 24°C) and fed two diets (control vs. Noni) in a 2 × 2 factorial design. Feed intake and body weights were recorded, and blood and liver samples were collected at 2 h and 3 weeks post-heat exposure. HS depressed feed intake, reduced body weight, and up regulated the hepatic expression of heat shock protein HSP60, HSP70, HSP90 as well as key lipogenic proteins (fatty acid synthase, FASN; acetyl co-A carboxylase alpha, ACCα and ATP citrate lyase, ACLY). HS down regulated the hepatic expression of lipoprotein lipase (LPL) and hepatic triacylglycerol lipase (LIPC), but up-regulated ATGL. Although it did not affect growth performance, Noni supplementation regulated the hepatic expression of lipogenic proteins in a time- and gene-specific manner. Prior to HS, Noni increased ACLY and FASN in the acute and chronic experimental conditions, respectively. During acute HS, Noni increased ACCα, but reduced FASN and ACLY expression. Under chronic HS, Noni up regulated ACCα and FASN but it down regulated ACLY. In vitro studies, using chicken hepatocyte cell lines, showed that HS down-regulated the expression of ACCα, FASN, and ACLY. Treatment with quercetin, one bioactive ingredient in Noni, up-regulated the expression of ACCα, FASN, and ACLY under TN conditions, but it appeared to down-regulate ACCα and increase ACLY levels under HS exposure. In conclusion, our findings indicate that HS induces hepatic lipogenesis in chickens and this effect is probably mediated via HSPs. The modulation of hepatic HSP expression suggest also that Noni might be involved in modulating the stress response in chicken liver.